5WIV

Structure of the sodium-bound human D4 Dopamine receptor in complex with Nemonapride


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.143 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

D4 dopamine receptor high-resolution structures enable the discovery of selective agonists.

Wang, S.Wacker, D.Levit, A.Che, T.Betz, R.M.McCorvy, J.D.Venkatakrishnan, A.J.Huang, X.P.Dror, R.O.Shoichet, B.K.Roth, B.L.

(2017) Science 358: 381-386

  • DOI: 10.1126/science.aan5468
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Dopamine receptors are implicated in the pathogenesis and treatment of nearly every neuropsychiatric disorder. Although thousands of drugs interact with these receptors, our molecular understanding of dopaminergic drug selectivity and design remains ...

    Dopamine receptors are implicated in the pathogenesis and treatment of nearly every neuropsychiatric disorder. Although thousands of drugs interact with these receptors, our molecular understanding of dopaminergic drug selectivity and design remains clouded. To illuminate dopamine receptor structure, function, and ligand recognition, we determined crystal structures of the D4 dopamine receptor in its inactive state bound to the antipsychotic drug nemonapride, with resolutions up to 1.95 angstroms. These structures suggest a mechanism for the control of constitutive signaling, and their unusually high resolution enabled a structure-based campaign for new agonists of the D4 dopamine receptor. The ability to efficiently exploit structure for specific probe discovery-rapidly moving from elucidating receptor structure to discovering previously unrecognized, selective agonists-testifies to the power of structure-based approaches.


    Organizational Affiliation

    Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7365, USA. shengunc@email.unc.edu dwacker@email.unc.edu bshoichet@gmail.com bryan_roth@med.unc.edu.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
D(4) dopamine receptor, soluble cytochrome b562 chimera
A
422Escherichia coliHomo sapiens
This entity is chimeric
Mutation(s): 3 
Gene Names: cybC, DRD4
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
G Protein-Coupled Receptors (GPCRs)
Protein: 
Dopamine D4 receptor complexed with nemonapride
Find proteins for P0ABE7 (Escherichia coli)
Go to UniProtKB:  P0ABE7
Find proteins for P21917 (Homo sapiens)
Go to Gene View: DRD4
Go to UniProtKB:  P21917
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
NA
Query on NA

Download SDF File 
Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
AQD
Query on AQD

Download SDF File 
Download CCD File 
A
Nemonapride
N-[(2R,3R)-1-benzyl-2-methylpyrrolidin-3-yl]-5-chloro-2-methoxy-4-(methylamino)benzamide
C21 H26 Cl N3 O2
KRVOJOCLBAAKSJ-RDTXWAMCSA-N
 Ligand Interaction
OLA
Query on OLA

Download SDF File 
Download CCD File 
A
OLEIC ACID
C18 H34 O2
ZQPPMHVWECSIRJ-KTKRTIGZSA-N
 Ligand Interaction
PEG
Query on PEG

Download SDF File 
Download CCD File 
A
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.143 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.195 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 67.861α = 90.00
b = 162.836β = 90.00
c = 83.181γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
PHASERphasing
HKL-2000data reduction
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Mental HealthUnited StatesR01MH112205
National Institutes of Health/National Institute of Mental HealthUnited StatesHHSN-271-2013-00017-C
National Institutes of Health/National Institute of Mental HealthUnited StatesU19MH082441
University of North CarolinaUnited StatesUNC Michael Hooker Chair for Protein Therapeutics and Translational Proteomics

Revision History 

  • Version 1.0: 2017-10-18
    Type: Initial release
  • Version 1.1: 2017-11-01
    Type: Database references
  • Version 1.2: 2018-01-17
    Type: Author supporting evidence